[gmx-users] simulation box

[Justin A. Lemkul]

Quoting Ricardo Soares <rsoares at fcfrp.usp.br>:

> noob noob wrote:
> >
> > Dear all,
> >
> >  I am new about MD simulation and I have some questions about the box
> > size.
> >
> > I had performed 1 simulation previously ( box size of 5 nm x 5 nm x 5
> > nm ) but now I change to a bigger molecules and increase the number of
> > molecules. So,the new system cannot fix into the previous box.
> > Therefore, I tried to Increase my box to a bigger one ( 20 nm x 20 nm
> > x 20 nm) which can fix the system nicely.
> >
> > So, is it compulsory to use certain box size in our system? or we just use
> > any box size which our molecules can fix into it, then perform MD?
> >
> Sorry, I didn't see this other question of yours.
> If you use a box that is much larger than the main molecule, you will
> need lots of water, which will be time-consuming. Otherwise, if you use
> a very small box, it may compromise the free movement of the protein.
> So i say the best option is to scale the box size according to your
> specific molecule size. This is done within the editconf program. (see
> the gromacs manual for further reference).
>

In addition, you need to consider cutoff lengths and periodic boundary
conditions/minimum image convention.  Some textbook reading is in order.

-Justin

> Cheers,
>
> Ricardo.
>
>
> > Sorry for the "stupid" questions.
> >
> > thanks for the comments.
> >
> >
> > Alvin Chan.
> > ------------------------------------------------------------------------
> > check out the rest of the Windows Live™. More than mail–Windows Live™
> > goes way beyond your inbox. More than messages
> > <http://www.microsoft.com/windows/windowslive/>
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> ___________________________________________________________
>
> Ricardo Oliveira dos Santos Soares
> Post-graduation Student in Biological Physics
> University of Sao Paulo - USP
> Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
> Phone: 55 (16) 3602-4840
> Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
> ___________________________________________________________
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================